The former Mainz 05 striker gave the Potters the lead in 28th minute. But, in the 44th minute, Chris Hughton’s men levelled matters through Pascal Gross before Kurt Zouma’s immediate response saw the visitors back in charge.
Huddersfield saw the ball more in the tie - posting an overall of 54 percent possession as opposed to the visitors' 46.
The game ended in a 2-2 draw after Jose Izquierdo struck past Lee Grant on the hour mark.
“To be honest, I'm a bit disappointed because I think today we should have won the game,” Choupo-Moting told club website.
“First half was better than the second half. I think in the second half we should have played more football. I don't know why but of course when you're away and you have a point you don't want to lose that point but I think we should have gone for the victory.
“Yes, it is never bad to get a point away but today we led two times I wanted to win. I'm a little disappointed I wanted to win but that's football. But at least we didn't lose.” he said.
Choupo-Moting ended a seven-game barren spell in front of goal - his last strikes coming against Manchester United on August 9 - with a well-executed finish off a sublime Xherdan Shaqiri assist.
"I'm happy about it. It was a good pass from Shaq [Shaqiri] and I think I controlled it good and at the end, it was a good finish," he said
“So, all in all, a good goal. I was looking forward since the Man U game and I'm happy that I scored today but more importantly [we couldn't get] the victory.”
He will be hoping to avoid another unproductive streak, starting from the Potters’ next league engagement against Crystal Place on Saturday.